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- PDB-4bq0: Pseudomonas aeruginosa beta-alanine:pyruvate aminotransferase hol... -

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Basic information

Entry
Database: PDB / ID: 4bq0
TitlePseudomonas aeruginosa beta-alanine:pyruvate aminotransferase holoenzyme without divalent cations on dimer-dimer interface
ComponentsBETA-ALANINE--PYRUVATE TRANSAMINASE
KeywordsTRANSFERASE / PSEUDO-TRANSLATION
Function / homology
Function and homology information


beta-alanine-pyruvate transaminase / beta-alanine:pyruvate transaminase activity / beta-alanine biosynthetic process / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Beta-alanine--pyruvate aminotransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsIsupov, M.N. / Lebedev, A.A. / Westlake, A. / Sayer, C. / Littlechild, J.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Space-Group and Origin Ambiguity in Macromolecular Structures with Pseudo-Symmetry and its Treatment with the Program Zanuda.
Authors: Lebedev, A.A. / Isupov, M.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural Studies of Pseudomonas and Chromobacterium Omega-Aminotransferases Provide Insights Into Their Differing Substrate Specificity.
Authors: Sayer, C. / Isupov, M.N. / Westlake, A. / Littlechild, J.A.
History
DepositionMay 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-ALANINE--PYRUVATE TRANSAMINASE
B: BETA-ALANINE--PYRUVATE TRANSAMINASE
C: BETA-ALANINE--PYRUVATE TRANSAMINASE
D: BETA-ALANINE--PYRUVATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,86212
Polymers193,7324
Non-polymers1,1308
Water30,1571674
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32910 Å2
ΔGint-178.1 kcal/mol
Surface area61300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.950, 192.180, 76.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99994, -0.01117, -0.00173), (-0.01108, 0.99905, -0.0421), (0.0022, -0.04208, -0.99911)-55.01466, 0.53675, 41.07166
2given(0.99989, 0.01281, -0.0077), (0.0128, -0.99992, -0.00036), (-0.00771, 0.00026, -0.99997)-0.44146, 121.44569, 38.21208
3given(-0.99999, 0.00218, 0.0041), (-0.00201, -0.99915, 0.04113), (0.00419, 0.04112, 0.99915)-55.8046, 120.17307, -2.3586

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Components

#1: Protein
BETA-ALANINE--PYRUVATE TRANSAMINASE / OMEGA AMINOTRANSFERASE


Mass: 48432.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q9I700
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1674 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPYRIDOXAL-5'-PHOSPHATE (PLP): COFACTOR PLP WAS NOT MODELLED TO FORM A SCHIFF BASE LINK ,INTERNAL ...PYRIDOXAL-5'-PHOSPHATE (PLP): COFACTOR PLP WAS NOT MODELLED TO FORM A SCHIFF BASE LINK ,INTERNAL ALDIMINE, TO THE CATALYTIC LYS288. THE OCCUPANCY REFINEMENT IN REFMAC HAS SHOWN THAT PROPORTION OF COFACTOR FORMING THE SCHIFF BASE TO LYS288 IS BELOW 0.3 IN ALL SUBUNITS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 41.9 % / Description: NONE
Crystal growMethod: microbatch / pH: 5.5
Details: 10 MG/ML PROTEIN, 50MM SODIUM CHLORIDE, 30 MM PYRUVATE, 100 MM SODIUM CITRATE, 20% W/V PEG 3000, PH 5.5, MICROBATCH CRYSTALLIZATION METHOD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.77→64 Å / Num. obs: 2104915 / % possible obs: 99 % / Redundancy: 13.2 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.3
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.1 / % possible all: 98.1

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data reduction
Aimlessdata scaling
MOLREPphasing
Zanudaphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B9B

4b9b


Resolution: 1.77→63.37 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.504 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27574 7988 5 %RANDOM
Rwork0.21584 ---
obs0.21886 151295 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.264 Å2
Baniso -1Baniso -2Baniso -3
1-4.85 Å20 Å20 Å2
2---2.87 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 1.77→63.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13292 0 68 1674 15034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914638
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9620037
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06952013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39424.071705
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.606152463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.76715107
X-RAY DIFFRACTIONr_chiral_restr0.10.22156
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111539
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2586.1877291
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.85410.399181
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.726.6587346
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.772→1.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 554 -
Rwork0.324 11027 -
obs--98.11 %

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